distance_matrix.h

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/* 
 * This file is part of biomcmc-lib, a low-level library for phylogenomic analysis.
 * Copyright (C) 2019-today  Leonardo de Oliveira Martins [ leomrtns at gmail.com;  http://www.leomartins.org ]
 *
 * biomcmc is free software; you can redistribute it and/or modify it under the terms of the GNU General Public
 * License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later
 * version.
 *
 * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied 
 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more 
 * details (file "COPYING" or http://www.gnu.org/copyleft/gpl.html).
 */

#ifndef _biomcmc_distance_matrix_h_
#define _biomcmc_distance_matrix_h_ 

#include "hashtable.h"

typedef struct distance_matrix_struct* distance_matrix;
typedef struct spdist_matrix_struct* spdist_matrix;

struct distance_matrix_struct
{
  int size;   
  double **d, 
         mean_K2P_dist, 
         var_K2P_dist,  
         mean_JC_dist,  
         mean_R,        
         var_R,         
         freq[20];      
  double *fromroot;     
  int *idx, *i_l, *i_r; 
  int ref_counter;
};

struct spdist_matrix_struct
{
  int size, n_missing;
  double *mean, *min; 
  int *count; 
  bool *species_present; 
  int ref_counter;
};

distance_matrix new_distance_matrix (int nseqs);
void zero_lower_distance_matrix (distance_matrix dist);
void transpose_distance_matrix (distance_matrix dist);
void del_distance_matrix (distance_matrix dist);

spdist_matrix new_spdist_matrix (int n_species);
void zero_all_spdist_matrix (spdist_matrix dist); 
void finalise_spdist_matrix (spdist_matrix dist);
void finalise_spdist_matrix_with_rescaling (spdist_matrix dist, double scale);
void complete_missing_spdist_from_global_spdist (spdist_matrix local, spdist_matrix global);
void copy_spdist_matrix_to_distance_matrix_upper (spdist_matrix spd, distance_matrix dist, bool use_means);
void del_spdist_matrix (spdist_matrix dist);


void fill_species_dists_from_gene_dists (distance_matrix spdist, distance_matrix gendist, int *sp_id, bool use_upper_gene);
void update_species_dists_from_spdist (distance_matrix global, distance_matrix local, int *spexist);

int prepare_spdistmatrix_from_gene_species_map (spdist_matrix spdist, int *sp_id, int n_sp_id);
void fill_spdistmatrix_from_gene_dists (spdist_matrix spdist, distance_matrix gendist, int *sp_id, bool use_upper_gene);
void fill_spdistmatrix_from_gene_dist_vector (spdist_matrix spdist, double *gdist, int n_gdist, int *sp_id);
void update_spdistmatrix_from_spdistmatrix (spdist_matrix global, spdist_matrix local);

#endif